Hi Murli,
I just now saw that your email went to not only my inbox, but also to
the bioconductor mailing list as well. I will now answer it here so
that others who may have similar questions can benefit:
Those are not actually errors. They are warnings. An error means
something severe went wrong and the code cannot (or should not)
continue. A warning means you should look at this message in case
this
detail might affect you.
The 1st of these warning messages is telling you that your file did
not
contain exon ranking information (and so the order is being inferred
by
the order that the exons are present in the source file). You may or
may not feel comfortable with that inference. Frankly, it depends on
the file (and the species of organism) whether or not its a fair thing
to assume and we expect that you will know whether or not you need to
worry about it.
The other warning says that your the code was unable to guess about
which (if any) of your chromosomes were circular.
Whether any of that is a problem or not will entirely depend on you
and
what you want (and what you want to do next). It's not possible for
us
to know whether or not these circumstances are a problem for you or
not,
so we issue a warning (instead of an error).
Marc
On 03/12/2014 02:27 PM, Maintainer wrote:
> Hi,
> I have run the function,makeTranscriptDbFromGFF, of the
GenomicFeatures package with the simplest way ï¼^txdb <-
makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format =
"gtf")ï¼0/00or other complicate way and always got the following
errors:
> Warning messages:
> 1: In .deduceExonRankings(exs, format = "gtf") :
> Infering Exon Rankings. If this is not what you expected, then
please be sure that you have provided a valid attribute for
exonRankAttributeName
> 2: In matchCircularity(chroms, circ_seqs) :
> None of the strings in your circ_seqs argument match your
seqnames.
> I got the gtf file of vitis vinefera from here:
> http://plants.ensembl.org/info/data/ftp/index.html.
>
> And I also tried the instructions of makeTranscriptDbFromGFF on
the website as the following:
> gtfFile <- system.file("extdata","Aedes_aegypti.partial.gtf",
package="GenomicFeatures")
> txdb <- makeTranscriptDbFromGFF(file = gtfFile, format= "gtf").
> Unfortunately, I got the same error as the vitis gtf file was
used.
> So I am confused. Why did the errors happen even if I use the
sample file?
> Thank you!
>
> -- output of sessionInfo():
>
> output
> txdb <- makeTranscriptDbFromGFF(file =
"Vitis_vinifera.IGGP_12x.gtf", format = "gtf")
> extracting transcript information
> Estimating transcript ranges.
> Extracting gene IDs
> Processing splicing information for gtf file.
> Deducing exon rank from relative coordinates provided
> Prepare the 'metadata' data frame ... metadata: OK
> Now generating chrominfo from available sequence names. No
chromosome length information is available.
> Warning messages:
> 1: In .deduceExonRankings(exs, format = "gtf") :
> Infering Exon Rankings. If this is not what you expected, then
please be sure that you have provided a valid attribute for
exonRankAttributeName
> 2: In matchCircularity(chroms, circ_seqs) :
> None of the strings in your circ_seqs argument match your
seqnames.
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_China.936
> [2] LC_CTYPE=Chinese (Simplified)_China.936
> [3] LC_MONETARY=Chinese (Simplified)_China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_China.936
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets
> [7] methods base
>
> other attached packages:
> [1] GenomicFeatures_1.14.3 AnnotationDbi_1.24.0
> [3] Biobase_2.22.0 GenomicRanges_1.14.4
> [5] XVector_0.2.0 IRanges_1.20.7
> [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6
> [4] BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1
> [7] Rsamtools_1.14.3 RSQLite_0.11.4 rtracklayer_1.22.4
> [10] stats4_3.0.2 tools_3.0.2 XML_3.98-1.1
> [13] zlibbioc_1.8.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
>
>
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